Background: For more than 25 years the golden mussel Limnoperna fortunei has been an aggressive invader in South America freshwaters, having travelled more than 5,000 km upstream across 5 countries. The mussel has outcompeted native species in the invaded environments and since chemicals in the water have been unable to control infestation in closed environments, it has economically harmed aquaculture, hydroelectric generation and ship transit. We sequenced the complete genome of the golden mussel to try to understand the molecular basis of its invasiveness and search for ways to control it. Findings: We have assembled the 1.6 Gb genome into 20548 scaffolds with a N50 length of 312 Kb using a hybrid and hierarchical assembly strategy from short and long DNA reads and transcriptomes. A total of 60717 coding genes were inferred from a customized transcriptome-trained AUGUSTUS run. We also compared predicted protein sets with those of complete molluscan genomes, revealing an exacerbation of protein-binding domains in L. fortunei . Conclusions: We assembled one of the best bivalve genomes available using a cost-effective approach using Illumina pair-end, mate pair and PacBio long reads. We expect the continuous and careful annotation of L. fortunei ’s genome to aid to the investigation of bivalve genetics, evolution and invasiveness, as well as the development of biotechnological tools for aquatic pest control.